Yes, most of the Airports of Ecuador started with SE, but in Flight Simulator 2002 there are lot of runways which starts Z09*, like Z09E for Banasur, Z09D for La Carolina, Z09L for La Judy South, Z09F for La Mina, Z09G for La Puntilla, Z09J for Patuca and Z09H for Puerto Villamil.

That probably means it's not even open to commercial use. Some airports in FS have scenery problems, like the ones thousands of feet above the surrounding terrain or others in a deep pit, so that could explain things.

One important point regarding these runways that most of these locations are relatively lower than the near ground, like a valley, but valley is within mountains these are big round dip in the ground. Right at this time I am not finding good words to explain